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<article doi="10.1016/j.molcel.2014.05.021" abstract="Mammalian cell homeostasis during starvation depends on initiation of autophagy by endoplasmic reticulum-localized phosphatidylinositol 3-phosphate (PtdIns(3)P) synthesis. Formation of double-membrane autophagosomes that engulf cytosolic components requires the LC3-conjugating Atg12-5-16L1 complex. The molecular mechanisms of Atg12-5-16L1 recruitment and significance of PtdIns(3)P synthesis at autophagosome formation sites are unknown. By identifying interacting partners of WIPIs, WD-repeat PtdIns(3)P effector proteins, we found that Atg16L1 directly binds WIPI2b. Mutation experiments and ectopic localization of WIPI2b to plasma membrane show that WIPI2b is a PtdIns(3)P effector upstream of Atg16L1 and is required for LC3 conjugation and starvation-induced autophagy through recruitment of the Atg12-5-16L1 complex. Atg16L1 mutants, which do not bind WIPI2b but bind FIP200, cannot rescue starvation-induced autophagy in Atg16L1-deficient MEFs. WIPI2b is also required for autophagic clearance of pathogenic bacteria. WIPI2b binds the membrane surrounding Salmonella and recruits the Atg12-5-16L1 complex, initiating LC3 conjugation, autophagosomal membrane formation, and engulfment of Salmonella."><fig id="4368"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4368"/><sd-panel panel_id="14303">(A) <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cell lines stably expressing <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI1a" ext_ids="55062" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI1a</sd-tag>, and <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> were incubated in full medium (F) or starvation medium (<sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>) (S) for 2 hr before being used for <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-TRAP <sd-tag id="sdTag18" source="sdapi" category="assay" entity_type="" role="" text="pull-down" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pull-down</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14303"/></sd-panel><sd-panel panel_id="14304">(B) <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> was <sd-tag id="sdTag33" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells treated with <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DSP" ext_ids="93313" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="57757-57-0" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">DSP</sd-tag>, at the indicated concentrations, before <sd-tag id="sdTag34" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14304"/></sd-panel><sd-panel panel_id="14237">(C) WT or <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> in fed medium or starved for 2 hr in <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> were fixed and labeled with an anti-<sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> antibody. Scale bars, 10 μm.(D) <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> puncta in (C) were counted, and a statistical analysis of <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> puncta was performed using an unpaired Student's t test. ∗p < 0.05. SEM for n = 3.<graphic href="https://api.sourcedata.io/file.php?panel_id=14237"/></sd-panel><sd-panel panel_id="14238">(E-H) <sd-tag id="sdTag44" source="sdapi" category="assay" entity_type="" role="" text="CLEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CLEM</sd-tag> (<sd-tag id="sdTag45" source="sdapi" category="assay" entity_type="" role="" text="correlative light and electron microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">correlative light and electron microscopy</sd-tag>) of endogenous <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> in <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag>.(E) Merged phase and confocal section of <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ cells labeled with anti-<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> antibody. Scale bar, 10 μm.(F) Low-magnification <sd-tag id="sdTag46" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> of cell in (E). Scale bar 10μm.(G and H) High magnification of boxed regions in (E) and (F). Top box and bottom box indicate panels (G) and (H), respectively. Arrows indicate open <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="phagophores" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">phagophores</sd-tag>. M, <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>; <sd-pretag id="sdPretag14424059678450" parent-tag-id="244">ER</sd-pretag>, <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endoplasmic reticulum" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endoplasmic reticulum</sd-tag>. Scale bars, 1 μm (G) and 0.5 μm (H).<graphic href="https://api.sourcedata.io/file.php?panel_id=14238"/></sd-panel><sd-panel panel_id="14239">(I and J) <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="cell_line" role="component" text="2GL9" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">2GL9</sd-tag> cells (<sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293</sd-tag> cells; Chan et al., 2007) were starved for 2 hr before visualization using indicated antibodies. Scale bars, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=14239"/></sd-panel><sd-panel panel_id="14240">(K) <sd-tag id="sdTag63" source="sdapi" category="assay" entity_type="" role="" text="Live-cell imaging" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Live-cell imaging</sd-tag> demonstrates that <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> translocates to <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag>-positive puncta in starvation. <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293</sd-tag> cells expressing <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> and <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> were starved in <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> and imaged every 2 s using a <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="spinning disk microscope" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">spinning disk microscope</sd-tag>. See also Figure S1 and Movie S1.<graphic href="https://api.sourcedata.io/file.php?panel_id=14240"/></sd-panel></fig><fig id="4369"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4369"/><sd-panel panel_id="14242">(B) Untransfected (UN) or <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> full-length (FL), 79-623, or 1-265 constructs were expressed in <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells stably expressing <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> and <sd-tag id="sdTag80" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> using <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-TRAP. Tags were visualized by <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. I, input; UB, unbound.<graphic href="https://api.sourcedata.io/file.php?panel_id=14242"/></sd-panel><sd-panel panel_id="14243">(C) <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="reporter" text="CFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CFP</sd-tag>-<sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg5" ext_ids="Q9H1Y0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg5</sd-tag>, <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1a" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1a</sd-tag>, and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> were transiently expressed in <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells. <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-tagged proteins were isolated using <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-TRAP and incubated with in vitro translated <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">35S</sd-tag>-labeled <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> constructs 1-265, 1-242, 1-230, and 1-207 before washing and analysis by <sd-tag id="sdTag90" source="sdapi" category="assay" entity_type="" role="" text="autoradiography" ext_ids="BAO_0002527" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="autoradiography" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">autoradiography</sd-tag>. Protein expression was validated by <sd-tag id="sdTag102" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> (bottom panel).<graphic href="https://api.sourcedata.io/file.php?panel_id=14243"/></sd-panel><sd-panel panel_id="14244">(D) Lysates from <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1a" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1a</sd-tag>, or <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> were mixed with lysates from <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> or <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L2" ext_ids="Q8NAA4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L2</sd-tag>. Protein complexes were <sd-tag id="sdTag113" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> using <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-TRAP, followed by <sd-tag id="sdTag116" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>. See also Figure S2 and Table S1.<graphic href="https://api.sourcedata.io/file.php?panel_id=14244"/></sd-panel></fig><fig id="4370"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4370"/><sd-panel panel_id="14247">(B) Lysates from <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transfected with <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> were mixed with lysates from <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transfected with <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L2" ext_ids="Q8NAA4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L2</sd-tag>, <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag>, or <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-<sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> mutants, <sd-tag id="sdTag129" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag>, and analyzed by <sd-tag id="sdTag130" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.(C) Statistical analysis of <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> binding in (B) was performed by Student's t test. SEM for n = 4. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14247"/></sd-panel><sd-panel panel_id="14248">(D) Cell lysates from <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L2" ext_ids="Q8NAA4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L2</sd-tag>, <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag>, or <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> mutants were subjected to <sd-tag id="sdTag144" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitation" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitation</sd-tag> using <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag> M2 agarose beads. Protein complexes were analyzed using <sd-tag id="sdTag143" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.(E) Statistical analysis of <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FIP200" ext_ids="Q8TDY2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="RB1CC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FIP200</sd-tag> binding in (D) was performed by Student's t test. SEM for n = 3. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14248"/></sd-panel><sd-panel panel_id="14249">(F) <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q80W47" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wipi2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> was <sd-tag id="sdTag150" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from lysates from WT or <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FIP200" ext_ids="12421" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Rb1cc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FIP200</sd-tag>−/− <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFS" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFS</sd-tag> after treatment with 0.5 mM <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="molecule" role="component" text="DSP" ext_ids="93313" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="57757-57-0" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">DSP</sd-tag>. Bound <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q8C0J2///Q6KAU8" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Atg16l1///Atg16l2" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Atg16</sd-tag> and <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg12" ext_ids="Q9CQY1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Atg12" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Atg12</sd-tag>-5 were detected by <sd-tag id="sdTag152" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14249"/></sd-panel><sd-panel panel_id="14250">(G) <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293</sd-tag> cells stably expressing <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> were and transiently transfected either <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> WT, E226R E230R (ERER), or D237R D239R (DRDR). Bound and input (bottom) were analyzed by <sd-tag id="sdTag160" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14250"/></sd-panel></fig><fig id="4371"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4371"/><sd-panel panel_id="14253">(A) Lysates from <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1a" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1a</sd-tag>, <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2a" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2a</sd-tag>, <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag>, or <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> FTTG mutant were used for <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-Trap. Endogenous <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> binding was analyzed by <sd-tag id="sdTag177" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.(B) Statistical analysis of (A) was performed by one-way ANOVA with Tukey's posttest. SEM for n = 3. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14253"/></sd-panel><sd-panel panel_id="14276">(D) <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-Trap from <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1a" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1a</sd-tag>, <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag>, <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> R108E, <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> R125E, or <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> R108E R125E was mixed with in vitro translated <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">35S</sd-tag>-labeled <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> and analyzed by <sd-tag id="sdTag196" source="sdapi" category="assay" entity_type="" role="" text="autoradiography" ext_ids="BAO_0002527" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="autoradiography" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">autoradiography</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14276"/></sd-panel><sd-panel panel_id="14279">(E) Lysates from <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag>, <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> ΔCT, <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2a" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2a</sd-tag>, <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1a" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1a</sd-tag>, or <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI1a" ext_ids="55062" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI1a</sd-tag> ΔCT were used for <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-Trap. Endogenous <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> binding was analyzed by <sd-tag id="sdTag213" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.(F) Statistical analysis of (E) was performed by one-way ANOVA with Tukey's posttest. SEM for n = 2. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14279"/></sd-panel><sd-panel panel_id="14282">(G) Lysates from <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> WT, <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> R108E, R125E, or R108E R125E were mixed with lysates from <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> WT, E226R, E230R, or E226R E230R in all possible permutations. Protein complexes from mixed lysates were <sd-tag id="sdTag223" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> using <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-Trap, followed by <sd-tag id="sdTag226" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.(H) Statistical analysis of (G) was performed by one-way ANOVA with Tukey's posttest. SEM from n = 3. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14282"/></sd-panel><sd-panel panel_id="14283">(I) <sd-tag id="sdTag231" source="sdapi" category="assay" entity_type="" role="" text="CLEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CLEM</sd-tag> analysis of <sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293</sd-tag> cells treated with siRNA to <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="gene" role="component" text="WIPI2" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2</sd-tag> were transfected with <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="gene" role="component" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> RERE and starved in <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>. Bright-field image (top), <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> RERE signal (middle), <sd-tag id="sdTag238" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> of selected cell (bottom). Boxed area shown in (J). Scale bars represent 10 μM for bright-field and confocal and 5 μM for <sd-tag id="sdTag239" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag>.(J) High-magnification <sd-tag id="sdTag240" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> of boxed area in (I). Arrows indicate open <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="phagophores" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">phagophores</sd-tag> in the vicinity of <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag> and <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> (M), which contain <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> RERE. See also Figures S4 and S5 and Table S1.<graphic href="https://api.sourcedata.io/file.php?panel_id=14283"/></sd-panel></fig><fig id="4372"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4372"/><sd-panel panel_id="14286">(A) <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, siRNA-resistant <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag>, or <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> RERE was expressed in <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells treated for 72 hr with either RISC-free (RF) or <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> siRNA. Cells were left in full medium (F) or starved for 2 hr with <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> (S) or <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> with <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BafA" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BafA</sd-tag> (B) before <sd-tag id="sdTag254" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.(B) Statistical analysis of (A). SEM for n = 3. Statistical analysis was performed by one-way ANOVA with Tukey's posttest. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14286"/></sd-panel><sd-panel panel_id="14292">(C) <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, siRNA-resistant <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag>, <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> RERE, <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> FTTG, or <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> FTTG RERE was expressed in <sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells treated for 72 hr with <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2</sd-tag> siRNA. Cells were left in full medium (F) or starved for 2 hr with <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> (S) or <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> with <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BafA" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BafA</sd-tag> (B) before <sd-tag id="sdTag274" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.(D) Statistical analysis of (C) was performed by one-way ANOVA with Tukey's posttest. The SEM for <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9GZQ8///Q9BXW4" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3B///MAP1LC3C" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (n = 2) and <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> (n = 4) are shown. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14292"/></sd-panel><sd-panel panel_id="14293">(E) siRNA-resistant <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag>, <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> RERE, <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag> FTTG, or <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> FTTG RERE was expressed in <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells treated for 72 hr with <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2</sd-tag> siRNA. Cells were starved in <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> for 2 hr without or with <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BafA" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BafA</sd-tag>, fixed, and labeled, and <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> was visualized by <sd-tag id="sdTag279" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bars, 10 μm.(F) Quantification of <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> puncta per cell from (E). SEM from 10 cells per condition; ∗∗∗p < 0.001 using one-way ANOVA.(G) Statistical analysis of <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta from (E) with <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> control (not shown in E). SEM for n = 3. Statistical analysis was performed by one-way ANOVA with Dunn's posttest t test. ∗p < 0.05. See also Table S1.<graphic href="https://api.sourcedata.io/file.php?panel_id=14293"/></sd-panel></fig><fig id="4373"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4373"/><sd-panel panel_id="14294">(A) <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing the indicated <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> constructs were treated in either full medium (F), starvation medium (S), or starvation medium with <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="wortmannin" ext_ids="CHEBI:52289" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="wortmannin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">wortmannin</sd-tag> (W) for 2 hr before <sd-tag id="sdTag299" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.(B) Statistical analysis of (A) was performed by one-way ANOVA with Tukey's post hoc test. SEM for n = 3. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14294"/></sd-panel><sd-panel panel_id="14295">(C) Complexes from <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells transiently expressing the indicated <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> constructs were <sd-tag id="sdTag310" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> using <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag>-Trap before analysis by <sd-tag id="sdTag312" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14295"/></sd-panel><sd-panel panel_id="14296">(D) <sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="cell_line" role="component" text="2GL9" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">2GL9</sd-tag> cells transiently expressing the indicated <sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> constructs treated as in (A) were fixed and visualized by <sd-tag id="sdTag318" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=14296"/></sd-panel><sd-panel panel_id="14297">(E) <sd-tag id="sdTag328" source="sdapi" category="assay" entity_type="" role="" text="CLEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CLEM</sd-tag> of <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> cells expressing <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag331" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag332" source="sdapi" category="entity" entity_type="gene" role="component" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> CAAX. Bright-field and confocal image merged (left), confocal of expressing cell (middle), low-magnification <sd-tag id="sdTag333" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> of cell of interest (right). Boxed area indicates <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> region showing colocalization of <sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag>. Scale bar, 10 μm (n = 3).(F) High-magnification <sd-tag id="sdTag337" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> showing <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> region boxed in (E). Magnified insets, in top right, show small <sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicular clusters" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicular clusters</sd-tag> under the <sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> detected in <sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>-<sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="gene" role="component" text="WIPI2b" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2b</sd-tag> CAAX, <sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> expressing cells but not in untransfected cells from a control experiment.<graphic href="https://api.sourcedata.io/file.php?panel_id=14297"/></sd-panel><sd-panel panel_id="14298">(G) <sd-tag id="sdTag348" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells treated with either RISC-free (RF), <sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> siRNA, or <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FIP200" ext_ids="12421" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Rb1cc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FIP200</sd-tag> siRNA for 72 hr before transfection with <sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2b" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2b</sd-tag>-CAAX were incubated in full medium (F), <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> (S), or <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> with <sd-tag id="sdTag352" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="wortmannin" ext_ids="CHEBI:52289" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="wortmannin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">wortmannin</sd-tag> (W) for 2 hr before <sd-tag id="sdTag353" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis. Please note that all <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag> constructs are FTTG mutants. See also Figure S6 and Table S1.<graphic href="https://api.sourcedata.io/file.php?panel_id=14298"/></sd-panel></fig><fig id="4374"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4374"/><sd-panel panel_id="14299">(A) <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ <sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transiently transfected with either mock, <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-tagged <sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q8C0J2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> WT, ERER, or DRDR. After 2 hr in <sd-tag id="sdTag364" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, cells were fixed and labeled with anti-<sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and anti-<sd-tag id="sdTag366" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag> antibodies and visualized by <sd-tag id="sdTag367" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bars, 20 μm.(B) Statistical analysis of (A) was performed using one-way ANOVA with Dunn's posttest. ∗p < 0.05. SEM for n = 3.<graphic href="https://api.sourcedata.io/file.php?panel_id=14299"/></sd-panel><sd-panel panel_id="14300">(C) <sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ <sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transiently transfected with either mock, <sd-tag id="sdTag371" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-tagged <sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q8C0J2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> WT, E226R E230R (ERER), or D237R D239R (DRDR) before analysis by <sd-tag id="sdTag372" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.(D) Statistical analysis of (C) was performed by one-way ANOVA with Tukey's post hoc test. SEM for n = 3. ∗p < 0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=14300"/></sd-panel><sd-panel panel_id="14301">(E) <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HEK293A" ext_ids="CVCL_6910" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293-A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293A</sd-tag> cells were treated with either RISC-free control or <sd-tag id="sdTag379" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WIPI2" ext_ids="26100" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI2</sd-tag> siRNA before infection with <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="organism" role="component" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (moi = 100) for 1 hr, labeled with anti-<sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag384" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI2" ext_ids="Q9Y4P8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI2</sd-tag>, and <sd-tag id="sdTag385" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> antibodies, and followed by confocal analysis. Scale bars, 5 μm.(F) Statistical analysis for (E) was performed using an unpaired Student's t test. ∗p < 0.05. SEM for n = 3.<graphic href="https://api.sourcedata.io/file.php?panel_id=14301"/></sd-panel><sd-panel panel_id="14302">(G) <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag>Δ/Δ <sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transiently transfected with <sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg16L1" ext_ids="77040" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg16L1</sd-tag> WT, <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag388" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L1" ext_ids="Q8C0J2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Atg16l1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Atg16L1</sd-tag> ERER, or <sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>-<sd-tag id="sdTag395" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16L2" ext_ids="Q6KAU8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Atg16l2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Atg16L2</sd-tag> DRDR 24 hr before being infected with <sd-tag id="sdTag396" source="sdapi" category="entity" entity_type="organism" role="component" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (moi = 25) for 1 hr, labeled with anti-<sd-tag id="sdTag397" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, anti-<sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag>, and anti-<sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag> antibodies, and followed by analysis by <sd-tag id="sdTag400" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bars, 5 μm.(H) Statistical analysis of (G) was performed by one-way ANOVA with Dunn's post hoc test. SEM for n = 4. ∗p < 0.05. See also Figure S7.<graphic href="https://api.sourcedata.io/file.php?panel_id=14302"/></sd-panel></fig></article>